Starting phenix.real_space_refine on Thu Jul 2 13:48:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ezm_31389/07_2026/7ezm_31389.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ezm_31389/07_2026/7ezm_31389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ezm_31389/07_2026/7ezm_31389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ezm_31389/07_2026/7ezm_31389.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ezm_31389/07_2026/7ezm_31389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ezm_31389/07_2026/7ezm_31389.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ezm_31389/07_2026/7ezm_31389.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ezm_31389/07_2026/7ezm_31389.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 5748 2.51 5 N 1524 2.21 5 O 1667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9008 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1850 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2362 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 12, 'TRANS': 291} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 2, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "G" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 421 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "P" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYS:plan-2': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 1.92, per 1000 atoms: 0.21 Number of scatterers: 9008 At special positions: 0 Unit cell: (104.5, 120.175, 121.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 1667 8.00 N 1524 7.00 C 5748 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 114 " - pdb=" SG CYS D 196 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 388.2 milliseconds 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2202 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 40.1% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 6 through 38 Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 212 through 221 removed outlier: 4.595A pdb=" N ILE A 217 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N HIS A 218 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 246 through 261 Processing helix chain 'A' and resid 262 through 266 removed outlier: 3.550A pdb=" N GLN A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN A 266 " --> pdb=" O TRP A 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 262 through 266' Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 301 through 315 Processing helix chain 'A' and resid 335 through 356 Processing helix chain 'B' and resid 6 through 26 removed outlier: 4.209A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'D' and resid 39 through 69 Processing helix chain 'D' and resid 70 through 73 Processing helix chain 'D' and resid 74 through 105 Proline residue: D 96 - end of helix Proline residue: D 101 - end of helix Processing helix chain 'D' and resid 110 through 145 Processing helix chain 'D' and resid 147 through 152 Processing helix chain 'D' and resid 154 through 173 Processing helix chain 'D' and resid 174 through 180 removed outlier: 3.595A pdb=" N ILE D 178 " --> pdb=" O THR D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 218 through 248 Processing helix chain 'D' and resid 301 through 339 Proline residue: D 328 - end of helix Processing helix chain 'D' and resid 339 through 348 Processing helix chain 'D' and resid 349 through 371 removed outlier: 4.019A pdb=" N SER D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) Proline residue: D 367 - end of helix Processing helix chain 'D' and resid 374 through 383 Processing helix chain 'G' and resid 9 through 25 removed outlier: 3.849A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 52 through 56 removed outlier: 4.106A pdb=" N GLY H 56 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 196 removed outlier: 6.662A pdb=" N LEU A 40 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 204 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU A 42 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A 225 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE A 226 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE A 272 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE A 228 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN A 274 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 230 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.882A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.675A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.354A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.814A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.649A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.827A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 184 through 186 Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.063A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.507A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2088 1.33 - 1.46: 2829 1.46 - 1.60: 4172 1.60 - 1.73: 1 1.73 - 1.86: 106 Bond restraints: 9196 Sorted by residual: bond pdb=" O1 TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.462 1.636 -0.174 2.00e-02 2.50e+03 7.56e+01 bond pdb=" OH TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.679 1.526 0.153 2.00e-02 2.50e+03 5.81e+01 bond pdb=" CA SER B 281 " pdb=" CB SER B 281 " ideal model delta sigma weight residual 1.532 1.465 0.066 1.78e-02 3.16e+03 1.39e+01 bond pdb=" N VAL A 240 " pdb=" CA VAL A 240 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.60e+00 bond pdb=" N GLY B 41 " pdb=" CA GLY B 41 " ideal model delta sigma weight residual 1.448 1.492 -0.044 1.88e-02 2.83e+03 5.56e+00 ... (remaining 9191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 11457 1.81 - 3.62: 914 3.62 - 5.43: 91 5.43 - 7.24: 18 7.24 - 9.05: 4 Bond angle restraints: 12484 Sorted by residual: angle pdb=" C ARG D 139 " pdb=" CA ARG D 139 " pdb=" CB ARG D 139 " ideal model delta sigma weight residual 110.68 118.72 -8.04 1.70e+00 3.46e-01 2.23e+01 angle pdb=" C ARG D 345 " pdb=" CA ARG D 345 " pdb=" CB ARG D 345 " ideal model delta sigma weight residual 110.88 103.83 7.05 1.57e+00 4.06e-01 2.02e+01 angle pdb=" N VAL A 238 " pdb=" CA VAL A 238 " pdb=" C VAL A 238 " ideal model delta sigma weight residual 109.20 102.41 6.79 1.55e+00 4.16e-01 1.92e+01 angle pdb=" N ALA H 136 " pdb=" CA ALA H 136 " pdb=" C ALA H 136 " ideal model delta sigma weight residual 113.02 107.99 5.03 1.20e+00 6.94e-01 1.75e+01 angle pdb=" CA VAL A 238 " pdb=" C VAL A 238 " pdb=" O VAL A 238 " ideal model delta sigma weight residual 121.92 117.04 4.88 1.17e+00 7.31e-01 1.74e+01 ... (remaining 12479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 4939 16.36 - 32.71: 413 32.71 - 49.06: 76 49.06 - 65.42: 22 65.42 - 81.77: 5 Dihedral angle restraints: 5455 sinusoidal: 2051 harmonic: 3404 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 156.95 -63.95 1 1.00e+01 1.00e-02 5.38e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 151.59 28.41 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 152.84 27.16 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 5452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1137 0.081 - 0.163: 272 0.163 - 0.244: 23 0.244 - 0.325: 3 0.325 - 0.407: 2 Chirality restraints: 1437 Sorted by residual: chirality pdb=" CA ARG A 210 " pdb=" N ARG A 210 " pdb=" C ARG A 210 " pdb=" CB ARG A 210 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CA ARG D 345 " pdb=" N ARG D 345 " pdb=" C ARG D 345 " pdb=" CB ARG D 345 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CG LEU A 316 " pdb=" CB LEU A 316 " pdb=" CD1 LEU A 316 " pdb=" CD2 LEU A 316 " both_signs ideal model delta sigma weight residual False -2.59 -2.86 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1434 not shown) Planarity restraints: 1576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 313 " 0.048 9.50e-02 1.11e+02 4.23e-02 1.69e+01 pdb=" NE ARG D 313 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ARG D 313 " 0.070 2.00e-02 2.50e+03 pdb=" NH1 ARG D 313 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG D 313 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 367 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C PRO D 367 " 0.071 2.00e-02 2.50e+03 pdb=" O PRO D 367 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE D 368 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 202 " -0.006 9.50e-02 1.11e+02 3.17e-02 1.25e+01 pdb=" NE ARG A 202 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 202 " -0.061 2.00e-02 2.50e+03 pdb=" NH1 ARG A 202 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG A 202 " 0.020 2.00e-02 2.50e+03 ... (remaining 1573 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1292 2.76 - 3.30: 9206 3.30 - 3.83: 15416 3.83 - 4.37: 19126 4.37 - 4.90: 32178 Nonbonded interactions: 77218 Sorted by model distance: nonbonded pdb=" OH TYR A 356 " pdb=" OE1 GLN D 153 " model vdw 2.228 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.239 3.040 nonbonded pdb=" O TYR D 360 " pdb=" OG SER D 363 " model vdw 2.247 3.040 nonbonded pdb=" O MET D 72 " pdb=" ND2 ASN D 77 " model vdw 2.248 3.120 nonbonded pdb=" OD1 ASN D 98 " pdb=" OH TYR D 360 " model vdw 2.260 3.040 ... (remaining 77213 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.790 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.174 9200 Z= 0.561 Angle : 1.074 9.054 12492 Z= 0.645 Chirality : 0.068 0.407 1437 Planarity : 0.009 0.102 1576 Dihedral : 13.160 81.772 3241 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.94 % Allowed : 3.34 % Favored : 95.72 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.23), residues: 1150 helix: -0.43 (0.23), residues: 404 sheet: -0.10 (0.30), residues: 278 loop : -0.83 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.071 0.009 ARG D 313 TYR 0.046 0.009 TYR H 175 PHE 0.025 0.006 PHE B 241 TRP 0.037 0.008 TRP B 82 HIS 0.019 0.006 HIS D 157 Details of bonding type rmsd/Z covalent geometry : bond 0.01068 / 0.56 ( 9196) covalent geometry : angle 1.07377 / 0.64 (12484) SS BOND : bond 0.01126 / 0.54 ( 4) SS BOND : angle 1.86097 / 0.95 ( 8) hydrogen bonds : bond 0.16802 / 10.94 ( 482) hydrogen bonds : angle 7.01862 / 4.93 ( 1335) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 308 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.7426 (p) cc_final: 0.6994 (p) REVERT: A 9 ASP cc_start: 0.6886 (m-30) cc_final: 0.6420 (m-30) REVERT: A 39 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6529 (mt-10) REVERT: A 237 GLN cc_start: 0.7324 (mt0) cc_final: 0.7085 (mt0) REVERT: A 275 LYS cc_start: 0.7832 (mttt) cc_final: 0.7624 (mttt) REVERT: B 67 SER cc_start: 0.7986 (m) cc_final: 0.7688 (t) REVERT: B 74 SER cc_start: 0.7782 (t) cc_final: 0.7473 (t) REVERT: B 98 SER cc_start: 0.7826 (p) cc_final: 0.7443 (t) REVERT: B 118 ASP cc_start: 0.6246 (p0) cc_final: 0.5987 (p0) REVERT: B 184 THR cc_start: 0.8506 (p) cc_final: 0.8297 (t) REVERT: B 220 GLN cc_start: 0.8247 (mt0) cc_final: 0.7890 (mt0) REVERT: B 221 THR cc_start: 0.7915 (m) cc_final: 0.7714 (t) REVERT: B 277 SER cc_start: 0.8359 (t) cc_final: 0.8151 (t) REVERT: B 334 SER cc_start: 0.7768 (m) cc_final: 0.7554 (p) REVERT: D 76 THR cc_start: 0.7375 (m) cc_final: 0.7143 (m) REVERT: D 111 SER cc_start: 0.8252 (t) cc_final: 0.8006 (p) REVERT: H 141 THR cc_start: 0.7753 (m) cc_final: 0.7420 (p) REVERT: H 180 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7688 (mtt180) outliers start: 9 outliers final: 4 residues processed: 315 average time/residue: 0.4133 time to fit residues: 140.2662 Evaluate side-chains 277 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 273 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 250 GLU Chi-restraints excluded: chain H residue 135 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 132 ASN D 131 ASN G 18 GLN H 142 GLN H 179 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.135313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.121251 restraints weight = 12315.272| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.93 r_work: 0.3350 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9200 Z= 0.178 Angle : 0.635 6.669 12492 Z= 0.335 Chirality : 0.045 0.156 1437 Planarity : 0.005 0.042 1576 Dihedral : 6.905 71.180 1271 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 4.70 % Allowed : 13.88 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.25), residues: 1150 helix: 1.31 (0.26), residues: 409 sheet: -0.24 (0.29), residues: 282 loop : -0.00 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 345 TYR 0.014 0.002 TYR H 190 PHE 0.033 0.002 PHE A 55 TRP 0.026 0.002 TRP B 339 HIS 0.006 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 ( 9196) covalent geometry : angle 0.63126 / 0.33 (12484) SS BOND : bond 0.00589 / 0.31 ( 4) SS BOND : angle 2.79145 / 1.38 ( 8) hydrogen bonds : bond 0.04348 / 2.86 ( 482) hydrogen bonds : angle 5.16241 / 3.64 ( 1335) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 271 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.8265 (p) cc_final: 0.7962 (p) REVERT: A 39 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7403 (mt-10) REVERT: A 201 PHE cc_start: 0.8362 (m-80) cc_final: 0.7857 (m-80) REVERT: A 212 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7728 (mt-10) REVERT: A 276 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7433 (ptpp) REVERT: A 290 ASP cc_start: 0.7636 (m-30) cc_final: 0.7407 (m-30) REVERT: B 52 ARG cc_start: 0.7764 (ttm110) cc_final: 0.7556 (ptp90) REVERT: B 68 ARG cc_start: 0.8133 (ttt180) cc_final: 0.7761 (ttt180) REVERT: B 98 SER cc_start: 0.7751 (p) cc_final: 0.7382 (t) REVERT: B 170 ASP cc_start: 0.7766 (t70) cc_final: 0.7395 (t0) REVERT: B 186 ASP cc_start: 0.7093 (t0) cc_final: 0.6845 (t0) REVERT: B 214 ARG cc_start: 0.7768 (mtm180) cc_final: 0.7537 (mtm-85) REVERT: B 268 ASN cc_start: 0.7656 (p0) cc_final: 0.7421 (p0) REVERT: B 271 CYS cc_start: 0.7856 (m) cc_final: 0.7540 (p) REVERT: D 126 SER cc_start: 0.8650 (OUTLIER) cc_final: 0.8403 (m) REVERT: D 202 ASN cc_start: 0.7888 (OUTLIER) cc_final: 0.7523 (p0) REVERT: D 308 LYS cc_start: 0.8256 (mmtp) cc_final: 0.7999 (mttm) REVERT: D 344 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7601 (mt-10) REVERT: H 78 THR cc_start: 0.8452 (t) cc_final: 0.7819 (m) REVERT: H 141 THR cc_start: 0.8020 (m) cc_final: 0.7613 (p) REVERT: H 180 ARG cc_start: 0.8380 (mtt180) cc_final: 0.8043 (mtt180) REVERT: P 8 PHE cc_start: 0.8445 (m-10) cc_final: 0.8200 (m-10) outliers start: 45 outliers final: 19 residues processed: 289 average time/residue: 0.4650 time to fit residues: 144.3554 Evaluate side-chains 256 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 234 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 0.0270 chunk 75 optimal weight: 0.5980 chunk 61 optimal weight: 0.1980 chunk 57 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 45 optimal weight: 0.2980 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 259 GLN D 77 ASN D 374 ASN H 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.137257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.123390 restraints weight = 12302.113| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.93 r_work: 0.3373 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9200 Z= 0.121 Angle : 0.560 7.310 12492 Z= 0.294 Chirality : 0.042 0.145 1437 Planarity : 0.004 0.042 1576 Dihedral : 5.481 70.903 1263 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.76 % Allowed : 17.75 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.25), residues: 1150 helix: 1.67 (0.26), residues: 417 sheet: -0.18 (0.29), residues: 286 loop : 0.10 (0.32), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 129 TYR 0.017 0.001 TYR D 179 PHE 0.030 0.001 PHE A 55 TRP 0.023 0.002 TRP B 339 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 9196) covalent geometry : angle 0.55810 / 0.29 (12484) SS BOND : bond 0.00828 / 0.33 ( 4) SS BOND : angle 2.05269 / 1.05 ( 8) hydrogen bonds : bond 0.03716 / 2.42 ( 482) hydrogen bonds : angle 4.81351 / 3.38 ( 1335) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 251 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.8324 (p) cc_final: 0.7964 (p) REVERT: A 9 ASP cc_start: 0.7975 (m-30) cc_final: 0.7632 (m-30) REVERT: A 39 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7409 (mt-10) REVERT: A 201 PHE cc_start: 0.8389 (m-80) cc_final: 0.7671 (m-80) REVERT: A 212 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7771 (mt-10) REVERT: A 256 ARG cc_start: 0.7770 (ttm-80) cc_final: 0.7562 (ttm-80) REVERT: A 276 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7448 (ptpp) REVERT: A 290 ASP cc_start: 0.7657 (m-30) cc_final: 0.7413 (m-30) REVERT: A 307 GLU cc_start: 0.7952 (tp30) cc_final: 0.7671 (tp30) REVERT: A 326 SER cc_start: 0.8627 (p) cc_final: 0.8405 (t) REVERT: B 33 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7567 (mt) REVERT: B 52 ARG cc_start: 0.7658 (ttm110) cc_final: 0.7304 (mtp85) REVERT: B 87 THR cc_start: 0.8082 (OUTLIER) cc_final: 0.7789 (t) REVERT: B 98 SER cc_start: 0.7812 (p) cc_final: 0.7486 (t) REVERT: B 137 ARG cc_start: 0.8047 (tpp-160) cc_final: 0.7838 (tpp-160) REVERT: B 170 ASP cc_start: 0.7747 (t70) cc_final: 0.7328 (t0) REVERT: B 212 ASP cc_start: 0.7688 (t70) cc_final: 0.7412 (t0) REVERT: B 227 SER cc_start: 0.8446 (t) cc_final: 0.8114 (t) REVERT: B 268 ASN cc_start: 0.7667 (p0) cc_final: 0.7423 (p0) REVERT: B 271 CYS cc_start: 0.8005 (m) cc_final: 0.7646 (p) REVERT: B 274 THR cc_start: 0.7833 (m) cc_final: 0.7608 (p) REVERT: D 126 SER cc_start: 0.8615 (t) cc_final: 0.8379 (m) REVERT: D 202 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7726 (p0) REVERT: D 227 VAL cc_start: 0.8313 (t) cc_final: 0.8112 (m) REVERT: D 308 LYS cc_start: 0.8222 (mmtp) cc_final: 0.7963 (mttp) REVERT: D 336 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7888 (ttt180) REVERT: D 344 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7600 (mt-10) REVERT: H 63 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.8146 (t) REVERT: P 8 PHE cc_start: 0.8360 (m-10) cc_final: 0.8134 (m-10) outliers start: 36 outliers final: 21 residues processed: 268 average time/residue: 0.4849 time to fit residues: 138.9346 Evaluate side-chains 269 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 242 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 202 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 304 ASN Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 154 SER Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 65 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.0010 chunk 104 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.135916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.121376 restraints weight = 12273.989| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.97 r_work: 0.3345 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9200 Z= 0.135 Angle : 0.553 6.777 12492 Z= 0.289 Chirality : 0.042 0.157 1437 Planarity : 0.004 0.041 1576 Dihedral : 5.270 70.501 1262 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.59 % Allowed : 17.95 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.25), residues: 1150 helix: 1.90 (0.26), residues: 411 sheet: -0.18 (0.29), residues: 283 loop : 0.08 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 38 TYR 0.017 0.001 TYR D 179 PHE 0.028 0.001 PHE A 55 TRP 0.019 0.001 TRP B 339 HIS 0.003 0.001 HIS D 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 9196) covalent geometry : angle 0.55106 / 0.29 (12484) SS BOND : bond 0.00646 / 0.34 ( 4) SS BOND : angle 1.93412 / 0.98 ( 8) hydrogen bonds : bond 0.03646 / 2.38 ( 482) hydrogen bonds : angle 4.67671 / 3.27 ( 1335) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 235 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.8435 (p) cc_final: 0.8180 (p) REVERT: A 9 ASP cc_start: 0.7924 (m-30) cc_final: 0.7608 (m-30) REVERT: A 39 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7384 (mt-10) REVERT: A 201 PHE cc_start: 0.8429 (m-80) cc_final: 0.7768 (m-80) REVERT: A 276 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7486 (ptpp) REVERT: A 290 ASP cc_start: 0.7683 (m-30) cc_final: 0.7362 (m-30) REVERT: A 307 GLU cc_start: 0.8109 (tp30) cc_final: 0.7734 (tp30) REVERT: A 322 LYS cc_start: 0.8024 (ttmt) cc_final: 0.7738 (ttmm) REVERT: A 326 SER cc_start: 0.8663 (p) cc_final: 0.8436 (t) REVERT: A 354 LYS cc_start: 0.8123 (mmmt) cc_final: 0.7847 (mmmt) REVERT: B 33 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7585 (mt) REVERT: B 52 ARG cc_start: 0.7659 (ttm110) cc_final: 0.7303 (mtp85) REVERT: B 87 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7773 (t) REVERT: B 98 SER cc_start: 0.7837 (p) cc_final: 0.7454 (t) REVERT: B 143 THR cc_start: 0.8542 (p) cc_final: 0.8323 (p) REVERT: B 170 ASP cc_start: 0.7897 (t70) cc_final: 0.7452 (t0) REVERT: B 212 ASP cc_start: 0.7706 (t70) cc_final: 0.7463 (t0) REVERT: B 221 THR cc_start: 0.8184 (m) cc_final: 0.7946 (t) REVERT: B 227 SER cc_start: 0.8478 (t) cc_final: 0.8115 (t) REVERT: B 271 CYS cc_start: 0.7986 (m) cc_final: 0.7688 (p) REVERT: B 274 THR cc_start: 0.7846 (m) cc_final: 0.7616 (p) REVERT: D 74 THR cc_start: 0.8055 (t) cc_final: 0.7684 (p) REVERT: D 126 SER cc_start: 0.8638 (t) cc_final: 0.8402 (m) REVERT: D 202 ASN cc_start: 0.8072 (p0) cc_final: 0.7832 (p0) REVERT: D 329 ILE cc_start: 0.8462 (tp) cc_final: 0.8245 (tt) REVERT: D 336 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7883 (ttt180) REVERT: D 344 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7672 (mt-10) REVERT: H 63 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8163 (t) outliers start: 44 outliers final: 19 residues processed: 258 average time/residue: 0.4788 time to fit residues: 132.6285 Evaluate side-chains 257 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 233 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 79 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.128668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.114429 restraints weight = 12169.925| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.92 r_work: 0.3309 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9200 Z= 0.180 Angle : 0.579 9.189 12492 Z= 0.300 Chirality : 0.043 0.157 1437 Planarity : 0.004 0.040 1576 Dihedral : 5.278 69.574 1262 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.70 % Allowed : 19.42 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.25), residues: 1150 helix: 1.82 (0.25), residues: 417 sheet: -0.16 (0.29), residues: 284 loop : -0.07 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 38 TYR 0.016 0.002 TYR D 179 PHE 0.025 0.002 PHE A 55 TRP 0.016 0.002 TRP B 339 HIS 0.005 0.001 HIS D 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 ( 9196) covalent geometry : angle 0.57706 / 0.30 (12484) SS BOND : bond 0.00769 / 0.40 ( 4) SS BOND : angle 2.08489 / 1.04 ( 8) hydrogen bonds : bond 0.03849 / 2.51 ( 482) hydrogen bonds : angle 4.71043 / 3.29 ( 1335) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 246 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.8465 (p) cc_final: 0.8188 (p) REVERT: A 9 ASP cc_start: 0.7946 (m-30) cc_final: 0.7633 (m-30) REVERT: A 39 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7220 (mt-10) REVERT: A 201 PHE cc_start: 0.8485 (m-80) cc_final: 0.7827 (m-80) REVERT: A 202 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.8008 (ttm-80) REVERT: A 290 ASP cc_start: 0.7714 (m-30) cc_final: 0.7378 (m-30) REVERT: A 307 GLU cc_start: 0.8078 (tp30) cc_final: 0.7730 (tp30) REVERT: A 322 LYS cc_start: 0.8067 (ttmt) cc_final: 0.7821 (ttmm) REVERT: A 326 SER cc_start: 0.8641 (p) cc_final: 0.8433 (t) REVERT: B 52 ARG cc_start: 0.7798 (ttm110) cc_final: 0.7459 (mtp85) REVERT: B 87 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7817 (t) REVERT: B 98 SER cc_start: 0.7977 (p) cc_final: 0.7636 (t) REVERT: B 212 ASP cc_start: 0.7711 (t70) cc_final: 0.7470 (t0) REVERT: B 221 THR cc_start: 0.8156 (m) cc_final: 0.7947 (t) REVERT: B 227 SER cc_start: 0.8493 (t) cc_final: 0.8112 (t) REVERT: B 271 CYS cc_start: 0.8055 (m) cc_final: 0.7778 (p) REVERT: B 312 ASP cc_start: 0.7608 (t0) cc_final: 0.7356 (t70) REVERT: D 74 THR cc_start: 0.8070 (t) cc_final: 0.7690 (p) REVERT: D 75 VAL cc_start: 0.8167 (p) cc_final: 0.7709 (t) REVERT: D 126 SER cc_start: 0.8647 (t) cc_final: 0.8408 (m) REVERT: D 202 ASN cc_start: 0.8150 (p0) cc_final: 0.7931 (p0) REVERT: D 227 VAL cc_start: 0.8438 (t) cc_final: 0.8233 (m) REVERT: D 329 ILE cc_start: 0.8450 (tp) cc_final: 0.8244 (tt) REVERT: D 336 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7951 (ttt180) REVERT: D 344 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7713 (mt-10) REVERT: H 63 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8165 (t) outliers start: 45 outliers final: 22 residues processed: 268 average time/residue: 0.4860 time to fit residues: 140.2545 Evaluate side-chains 261 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 236 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 6 optimal weight: 0.0060 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 0.0270 chunk 25 optimal weight: 0.0070 chunk 99 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 overall best weight: 0.3072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.131374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.117422 restraints weight = 12133.567| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.91 r_work: 0.3367 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9200 Z= 0.113 Angle : 0.540 8.699 12492 Z= 0.279 Chirality : 0.041 0.140 1437 Planarity : 0.004 0.039 1576 Dihedral : 5.153 70.990 1262 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.55 % Allowed : 21.92 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.25), residues: 1150 helix: 2.09 (0.26), residues: 410 sheet: -0.22 (0.29), residues: 287 loop : -0.05 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 38 TYR 0.016 0.001 TYR D 179 PHE 0.026 0.001 PHE A 55 TRP 0.017 0.001 TRP B 339 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 9196) covalent geometry : angle 0.53854 / 0.28 (12484) SS BOND : bond 0.00400 / 0.19 ( 4) SS BOND : angle 1.67974 / 0.85 ( 8) hydrogen bonds : bond 0.03497 / 2.27 ( 482) hydrogen bonds : angle 4.60444 / 3.21 ( 1335) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.8452 (p) cc_final: 0.8149 (p) REVERT: A 9 ASP cc_start: 0.7888 (m-30) cc_final: 0.7606 (m-30) REVERT: A 39 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7274 (mt-10) REVERT: A 201 PHE cc_start: 0.8469 (m-80) cc_final: 0.7683 (m-80) REVERT: A 290 ASP cc_start: 0.7701 (m-30) cc_final: 0.7357 (m-30) REVERT: A 307 GLU cc_start: 0.8026 (tp30) cc_final: 0.7701 (tp30) REVERT: A 322 LYS cc_start: 0.8047 (ttmt) cc_final: 0.7786 (ttmm) REVERT: B 52 ARG cc_start: 0.7686 (ttm110) cc_final: 0.7103 (mtt90) REVERT: B 87 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7766 (t) REVERT: B 98 SER cc_start: 0.7967 (p) cc_final: 0.7603 (t) REVERT: B 170 ASP cc_start: 0.7959 (t70) cc_final: 0.7539 (t0) REVERT: B 212 ASP cc_start: 0.7717 (t70) cc_final: 0.7470 (t0) REVERT: B 227 SER cc_start: 0.8481 (t) cc_final: 0.8081 (t) REVERT: B 271 CYS cc_start: 0.8032 (m) cc_final: 0.7821 (p) REVERT: B 312 ASP cc_start: 0.7560 (t0) cc_final: 0.7321 (t70) REVERT: D 74 THR cc_start: 0.8061 (t) cc_final: 0.7708 (p) REVERT: D 75 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7607 (t) REVERT: D 126 SER cc_start: 0.8623 (t) cc_final: 0.8398 (m) REVERT: D 161 VAL cc_start: 0.8139 (t) cc_final: 0.7870 (t) REVERT: D 202 ASN cc_start: 0.8173 (p0) cc_final: 0.7938 (p0) REVERT: D 329 ILE cc_start: 0.8447 (tp) cc_final: 0.8234 (tt) REVERT: D 336 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7875 (ttt180) REVERT: H 67 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7750 (ttp80) outliers start: 34 outliers final: 20 residues processed: 254 average time/residue: 0.5291 time to fit residues: 144.1025 Evaluate side-chains 263 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 240 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 109 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 70 optimal weight: 0.4980 chunk 85 optimal weight: 0.0770 chunk 99 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.129948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.116024 restraints weight = 12197.345| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.89 r_work: 0.3360 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9200 Z= 0.143 Angle : 0.556 8.221 12492 Z= 0.286 Chirality : 0.042 0.178 1437 Planarity : 0.004 0.038 1576 Dihedral : 5.136 70.092 1262 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.28 % Allowed : 21.40 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.25), residues: 1150 helix: 2.08 (0.25), residues: 410 sheet: -0.29 (0.29), residues: 289 loop : -0.07 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 38 TYR 0.018 0.001 TYR D 179 PHE 0.028 0.001 PHE A 55 TRP 0.015 0.001 TRP A 216 HIS 0.003 0.001 HIS D 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 9196) covalent geometry : angle 0.55390 / 0.29 (12484) SS BOND : bond 0.00675 / 0.34 ( 4) SS BOND : angle 1.75696 / 0.89 ( 8) hydrogen bonds : bond 0.03604 / 2.34 ( 482) hydrogen bonds : angle 4.60886 / 3.21 ( 1335) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 245 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.8473 (p) cc_final: 0.8212 (p) REVERT: A 9 ASP cc_start: 0.7931 (m-30) cc_final: 0.7675 (m-30) REVERT: A 10 LYS cc_start: 0.8436 (mtmm) cc_final: 0.8159 (mtmm) REVERT: A 39 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7193 (mt-10) REVERT: A 201 PHE cc_start: 0.8488 (m-80) cc_final: 0.7683 (m-80) REVERT: A 290 ASP cc_start: 0.7690 (m-30) cc_final: 0.7345 (m-30) REVERT: A 307 GLU cc_start: 0.7951 (tp30) cc_final: 0.7662 (tp30) REVERT: A 322 LYS cc_start: 0.8010 (ttmt) cc_final: 0.7763 (ttmm) REVERT: A 341 PHE cc_start: 0.8530 (t80) cc_final: 0.8082 (t80) REVERT: B 52 ARG cc_start: 0.7782 (ttm110) cc_final: 0.7253 (mtt90) REVERT: B 87 THR cc_start: 0.8002 (OUTLIER) cc_final: 0.7764 (t) REVERT: B 98 SER cc_start: 0.7998 (p) cc_final: 0.7615 (t) REVERT: B 170 ASP cc_start: 0.7944 (t70) cc_final: 0.7533 (t0) REVERT: B 212 ASP cc_start: 0.7730 (t70) cc_final: 0.7467 (t0) REVERT: B 227 SER cc_start: 0.8504 (t) cc_final: 0.8098 (t) REVERT: B 271 CYS cc_start: 0.8020 (m) cc_final: 0.7717 (p) REVERT: B 312 ASP cc_start: 0.7580 (t0) cc_final: 0.7326 (t70) REVERT: D 74 THR cc_start: 0.8017 (t) cc_final: 0.7705 (p) REVERT: D 75 VAL cc_start: 0.8108 (OUTLIER) cc_final: 0.7643 (t) REVERT: D 126 SER cc_start: 0.8655 (t) cc_final: 0.8433 (m) REVERT: D 202 ASN cc_start: 0.8194 (p0) cc_final: 0.7988 (p0) REVERT: D 329 ILE cc_start: 0.8439 (tp) cc_final: 0.8227 (tt) REVERT: D 336 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7865 (ttt180) REVERT: H 30 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.8197 (t) REVERT: H 67 ARG cc_start: 0.8195 (ttp80) cc_final: 0.7905 (ttp80) REVERT: P 8 PHE cc_start: 0.8486 (m-10) cc_final: 0.8269 (m-10) outliers start: 41 outliers final: 27 residues processed: 264 average time/residue: 0.4951 time to fit residues: 140.0692 Evaluate side-chains 268 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 63 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 97 optimal weight: 0.0020 chunk 33 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 77 ASN H 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.130216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.116165 restraints weight = 12103.261| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.91 r_work: 0.3361 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9200 Z= 0.141 Angle : 0.564 8.041 12492 Z= 0.289 Chirality : 0.042 0.195 1437 Planarity : 0.004 0.038 1576 Dihedral : 5.095 70.169 1262 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.65 % Allowed : 22.34 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.25), residues: 1150 helix: 2.07 (0.25), residues: 410 sheet: -0.26 (0.29), residues: 287 loop : -0.11 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 38 TYR 0.017 0.001 TYR D 179 PHE 0.031 0.001 PHE A 55 TRP 0.014 0.001 TRP B 339 HIS 0.003 0.001 HIS D 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 9196) covalent geometry : angle 0.56219 / 0.29 (12484) SS BOND : bond 0.00709 / 0.36 ( 4) SS BOND : angle 1.74096 / 0.89 ( 8) hydrogen bonds : bond 0.03599 / 2.33 ( 482) hydrogen bonds : angle 4.59694 / 3.20 ( 1335) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.8523 (p) cc_final: 0.8249 (p) REVERT: A 9 ASP cc_start: 0.7912 (m-30) cc_final: 0.7653 (m-30) REVERT: A 10 LYS cc_start: 0.8398 (mtmm) cc_final: 0.8122 (mtmm) REVERT: A 39 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7168 (mt-10) REVERT: A 201 PHE cc_start: 0.8493 (m-80) cc_final: 0.7634 (m-80) REVERT: A 202 ARG cc_start: 0.8346 (ttm-80) cc_final: 0.8065 (ttm-80) REVERT: A 290 ASP cc_start: 0.7689 (m-30) cc_final: 0.7365 (m-30) REVERT: A 307 GLU cc_start: 0.7973 (tp30) cc_final: 0.7657 (tp30) REVERT: A 322 LYS cc_start: 0.8076 (ttmt) cc_final: 0.7795 (ttmp) REVERT: A 341 PHE cc_start: 0.8531 (t80) cc_final: 0.8089 (t80) REVERT: B 52 ARG cc_start: 0.7742 (ttm110) cc_final: 0.7310 (mtp85) REVERT: B 87 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7747 (t) REVERT: B 98 SER cc_start: 0.8121 (p) cc_final: 0.7726 (t) REVERT: B 170 ASP cc_start: 0.7959 (t70) cc_final: 0.7522 (t0) REVERT: B 212 ASP cc_start: 0.7702 (t70) cc_final: 0.7451 (t0) REVERT: B 227 SER cc_start: 0.8475 (t) cc_final: 0.8229 (t) REVERT: B 228 ASP cc_start: 0.8026 (p0) cc_final: 0.7734 (p0) REVERT: B 258 ASP cc_start: 0.7572 (m-30) cc_final: 0.7282 (t0) REVERT: B 271 CYS cc_start: 0.8003 (m) cc_final: 0.7712 (p) REVERT: B 312 ASP cc_start: 0.7579 (t0) cc_final: 0.7309 (t70) REVERT: D 74 THR cc_start: 0.8005 (t) cc_final: 0.7660 (p) REVERT: D 75 VAL cc_start: 0.8140 (OUTLIER) cc_final: 0.7659 (t) REVERT: D 115 LYS cc_start: 0.8424 (mmmt) cc_final: 0.7597 (mmpt) REVERT: D 126 SER cc_start: 0.8655 (t) cc_final: 0.8418 (m) REVERT: D 213 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8036 (mp) REVERT: D 329 ILE cc_start: 0.8434 (tp) cc_final: 0.8221 (tt) REVERT: D 336 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7856 (ttt180) REVERT: H 30 SER cc_start: 0.8414 (OUTLIER) cc_final: 0.8193 (t) REVERT: H 67 ARG cc_start: 0.8208 (ttp80) cc_final: 0.7878 (ttp80) outliers start: 35 outliers final: 25 residues processed: 251 average time/residue: 0.5197 time to fit residues: 139.5938 Evaluate side-chains 264 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.128025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.113860 restraints weight = 12158.618| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.92 r_work: 0.3320 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9200 Z= 0.174 Angle : 0.593 8.497 12492 Z= 0.302 Chirality : 0.043 0.190 1437 Planarity : 0.004 0.039 1576 Dihedral : 5.110 69.548 1262 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.76 % Allowed : 22.03 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.25), residues: 1150 helix: 1.99 (0.25), residues: 410 sheet: -0.35 (0.29), residues: 297 loop : -0.16 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 38 TYR 0.016 0.002 TYR D 179 PHE 0.032 0.002 PHE A 55 TRP 0.016 0.002 TRP A 216 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 9196) covalent geometry : angle 0.59097 / 0.30 (12484) SS BOND : bond 0.00794 / 0.41 ( 4) SS BOND : angle 1.80444 / 0.91 ( 8) hydrogen bonds : bond 0.03789 / 2.47 ( 482) hydrogen bonds : angle 4.65767 / 3.24 ( 1335) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 240 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.8520 (p) cc_final: 0.8214 (p) REVERT: A 9 ASP cc_start: 0.7939 (m-30) cc_final: 0.7643 (m-30) REVERT: A 10 LYS cc_start: 0.8468 (mtmm) cc_final: 0.8191 (mtmm) REVERT: A 39 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7190 (mt-10) REVERT: A 201 PHE cc_start: 0.8536 (m-80) cc_final: 0.7685 (m-80) REVERT: A 290 ASP cc_start: 0.7716 (m-30) cc_final: 0.7404 (m-30) REVERT: A 307 GLU cc_start: 0.8004 (tp30) cc_final: 0.7684 (tp30) REVERT: A 322 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7819 (ttmm) REVERT: B 52 ARG cc_start: 0.7792 (ttm110) cc_final: 0.7376 (mtp85) REVERT: B 87 THR cc_start: 0.8019 (OUTLIER) cc_final: 0.7791 (t) REVERT: B 98 SER cc_start: 0.8170 (p) cc_final: 0.7789 (t) REVERT: B 212 ASP cc_start: 0.7719 (t70) cc_final: 0.7460 (t0) REVERT: B 221 THR cc_start: 0.8283 (t) cc_final: 0.8061 (m) REVERT: B 227 SER cc_start: 0.8556 (t) cc_final: 0.8302 (t) REVERT: B 228 ASP cc_start: 0.8027 (p0) cc_final: 0.7734 (p0) REVERT: B 258 ASP cc_start: 0.7570 (m-30) cc_final: 0.7259 (t0) REVERT: B 271 CYS cc_start: 0.8025 (m) cc_final: 0.7724 (p) REVERT: B 312 ASP cc_start: 0.7608 (t0) cc_final: 0.7350 (t70) REVERT: D 74 THR cc_start: 0.7996 (t) cc_final: 0.7655 (p) REVERT: D 75 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.7777 (t) REVERT: D 115 LYS cc_start: 0.8475 (mmmt) cc_final: 0.7675 (mmpt) REVERT: D 126 SER cc_start: 0.8653 (t) cc_final: 0.8413 (m) REVERT: D 170 PHE cc_start: 0.7155 (m-10) cc_final: 0.6821 (m-10) REVERT: D 213 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8050 (mp) REVERT: D 329 ILE cc_start: 0.8430 (tp) cc_final: 0.8217 (tt) REVERT: D 336 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7976 (ttt180) REVERT: H 30 SER cc_start: 0.8433 (OUTLIER) cc_final: 0.8215 (t) outliers start: 36 outliers final: 24 residues processed: 255 average time/residue: 0.4931 time to fit residues: 134.7653 Evaluate side-chains 265 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 107 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.115886 restraints weight = 12098.323| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.89 r_work: 0.3361 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9200 Z= 0.144 Angle : 0.582 8.703 12492 Z= 0.297 Chirality : 0.043 0.208 1437 Planarity : 0.004 0.039 1576 Dihedral : 5.057 70.341 1262 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.34 % Allowed : 22.65 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.25), residues: 1150 helix: 2.00 (0.25), residues: 410 sheet: -0.29 (0.30), residues: 282 loop : -0.12 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 38 TYR 0.016 0.001 TYR D 179 PHE 0.034 0.002 PHE A 55 TRP 0.013 0.001 TRP B 339 HIS 0.003 0.001 HIS D 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 9196) covalent geometry : angle 0.58070 / 0.30 (12484) SS BOND : bond 0.00685 / 0.35 ( 4) SS BOND : angle 1.62476 / 0.82 ( 8) hydrogen bonds : bond 0.03688 / 2.39 ( 482) hydrogen bonds : angle 4.65271 / 3.23 ( 1335) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2300 Ramachandran restraints generated. 1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.8513 (p) cc_final: 0.8223 (p) REVERT: A 9 ASP cc_start: 0.7880 (m-30) cc_final: 0.7629 (m-30) REVERT: A 10 LYS cc_start: 0.8435 (mtmm) cc_final: 0.8169 (mtmm) REVERT: A 201 PHE cc_start: 0.8532 (m-80) cc_final: 0.7734 (m-80) REVERT: A 290 ASP cc_start: 0.7705 (m-30) cc_final: 0.7384 (m-30) REVERT: A 307 GLU cc_start: 0.7982 (tp30) cc_final: 0.7665 (tp30) REVERT: A 322 LYS cc_start: 0.8111 (ttmt) cc_final: 0.7832 (ttmm) REVERT: B 52 ARG cc_start: 0.7746 (ttm110) cc_final: 0.7350 (mtp85) REVERT: B 87 THR cc_start: 0.7975 (OUTLIER) cc_final: 0.7744 (t) REVERT: B 98 SER cc_start: 0.8175 (p) cc_final: 0.7805 (t) REVERT: B 170 ASP cc_start: 0.7948 (t70) cc_final: 0.7512 (t0) REVERT: B 212 ASP cc_start: 0.7685 (t70) cc_final: 0.7448 (t0) REVERT: B 227 SER cc_start: 0.8500 (t) cc_final: 0.8111 (t) REVERT: B 246 ASP cc_start: 0.7811 (m-30) cc_final: 0.7489 (m-30) REVERT: B 258 ASP cc_start: 0.7532 (m-30) cc_final: 0.7240 (t0) REVERT: B 271 CYS cc_start: 0.7999 (m) cc_final: 0.7780 (p) REVERT: B 312 ASP cc_start: 0.7579 (t0) cc_final: 0.7346 (t70) REVERT: D 74 THR cc_start: 0.7923 (t) cc_final: 0.7585 (p) REVERT: D 75 VAL cc_start: 0.8228 (OUTLIER) cc_final: 0.7799 (t) REVERT: D 126 SER cc_start: 0.8659 (t) cc_final: 0.8433 (m) REVERT: D 170 PHE cc_start: 0.7153 (m-10) cc_final: 0.6804 (m-10) REVERT: D 213 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8026 (mp) REVERT: D 329 ILE cc_start: 0.8412 (tp) cc_final: 0.8194 (tt) REVERT: D 336 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7927 (ttt180) REVERT: H 30 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.8205 (t) REVERT: H 67 ARG cc_start: 0.8289 (ttp80) cc_final: 0.7803 (ttp80) outliers start: 32 outliers final: 26 residues processed: 257 average time/residue: 0.5236 time to fit residues: 143.9889 Evaluate side-chains 268 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 241 LYS Chi-restraints excluded: chain D residue 306 MET Chi-restraints excluded: chain D residue 336 ARG Chi-restraints excluded: chain D residue 350 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 15 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 46 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.129487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.115556 restraints weight = 11985.416| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.85 r_work: 0.3354 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9200 Z= 0.155 Angle : 0.590 8.454 12492 Z= 0.301 Chirality : 0.043 0.201 1437 Planarity : 0.004 0.039 1576 Dihedral : 5.029 70.003 1262 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.44 % Allowed : 23.80 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.26), residues: 1150 helix: 2.00 (0.25), residues: 410 sheet: -0.31 (0.30), residues: 292 loop : -0.13 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 38 TYR 0.019 0.002 TYR D 179 PHE 0.044 0.002 PHE A 55 TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS D 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 9196) covalent geometry : angle 0.58858 / 0.30 (12484) SS BOND : bond 0.00701 / 0.36 ( 4) SS BOND : angle 1.81616 / 0.91 ( 8) hydrogen bonds : bond 0.03709 / 2.41 ( 482) hydrogen bonds : angle 4.66640 / 3.24 ( 1335) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3583.59 seconds wall clock time: 61 minutes 57.01 seconds (3717.01 seconds total)